I agree, pads and Expedition PCB have pin swapping built in just fine. I/O Designer adds a rules aware unraveling of FPGA connections on a larger scale. It also adds automation to the FPGA design process to tie together everything from HDL to schematic to layout and back. It performs layout aware optimization of signal to pin assignments, automatic updating of your connections in the schematic, auto generated part and symbol sets for your FPGA, and other cool stuff. To summarize, the supercharged Corvette of FPGA designs on a PCB.